About the project

Oppisinpa kayttamaan RStudiota ja GitHubia! Kurssi vaikuttaa tosi hyvalta :)

Mun GitHub repository: https://github.com/SinaHulkkonen/IODS-project

Write a short description about the course and add a link to your github repository here. This is an R markdown (.Rmd) file so you can use R markdown syntax. See the ‘Useful links’ page in the mooc area (chapter 1) for instructions.

IODS week2 RStudio exercise

Sina Hulkkonen 08/11/2018

Describe the work you have done this week and summarize your learning.

I did all the DataCamp exercises for this week. I had huge problems with GitHub, I hope it is working now. I think I learned a lot!

Data.

#getting the data
students2014<-read.csv("http://s3.amazonaws.com/assets.datacamp.com/production/course_2218/datasets/learning2014.txt", sep=",", header=TRUE)

#inspecting the structre and dimensions
str(students2014)

## 'data.frame':    166 obs. of  7 variables:
##  $ gender  : Factor w/ 2 levels "F","M": 1 2 1 2 2 1 2 1 2 1 ...
##  $ age     : int  53 55 49 53 49 38 50 37 37 42 ...
##  $ attitude: num  3.7 3.1 2.5 3.5 3.7 3.8 3.5 2.9 3.8 2.1 ...
##  $ deep    : num  3.58 2.92 3.5 3.5 3.67 ...
##  $ stra    : num  3.38 2.75 3.62 3.12 3.62 ...
##  $ surf    : num  2.58 3.17 2.25 2.25 2.83 ...
##  $ points  : int  25 12 24 10 22 21 21 31 24 26 ...

dim(students2014)

## [1] 166   7

Students2014 is a dataset with 166 observations in 7 variables. It includes data of 166 students, their attitudes, answers on questions about their learning and the points they get.

Graphical overwiew of the data.

library(GGally)
library(ggplot2)

# getting to know the data, stratified by gender
p <- ggpairs(students2014, mapping = aes(col=gender, alpha=0.3), lower = list(combo = wrap("facethist", bins = 20)))

# draw the plot
p

The pink colour is for females and the blue colour for males. The figures show their distributions and how the variables correlate with each other, stratified by gender. For example, it seems that majority of the variables are normally distributed and that attitude and points have the strongest correlation with each other.

Multiple linear regression model

#I chose variables attiture, stra and surf, based on the previous section
my_model <- lm(points ~ attitude + stra + surf, data = students2014)
summary(my_model)

## 
## Call:
## lm(formula = points ~ attitude + stra + surf, data = students2014)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -17.1550  -3.4346   0.5156   3.6401  10.8952 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  11.0171     3.6837   2.991  0.00322 ** 
## attitude      3.3952     0.5741   5.913 1.93e-08 ***
## stra          0.8531     0.5416   1.575  0.11716    
## surf         -0.5861     0.8014  -0.731  0.46563    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 5.296 on 162 degrees of freedom
## Multiple R-squared:  0.2074, Adjusted R-squared:  0.1927 
## F-statistic: 14.13 on 3 and 162 DF,  p-value: 3.156e-08

#stra and surf didn't correlate statistically significantly with points, so they are removed in this model
my_model <- lm(points ~ attitude, data = students2014)
summary(my_model)

## 
## Call:
## lm(formula = points ~ attitude, data = students2014)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -16.9763  -3.2119   0.4339   4.1534  10.6645 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  11.6372     1.8303   6.358 1.95e-09 ***
## attitude      3.5255     0.5674   6.214 4.12e-09 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 5.32 on 164 degrees of freedom
## Multiple R-squared:  0.1906, Adjusted R-squared:  0.1856 
## F-statistic: 38.61 on 1 and 164 DF,  p-value: 4.119e-09

Linear regression model was applied to test if there is a linear correlation with dependent variable points by explanatory variables attitude, stra and surf.

In the first model with all of these three explanatory variables, only attitude explains points statistically significantly. In the firs model, when attitude increases by one, points increases by 3.5, in the second model when attitude increases by one, points increases by 3.4. This also tells that the proportion of points which was explained by the variables stra and surf is minimal.

R-squared tells us how close the data are to the fitted regression line. It is 19% in both models, which means that they practically model this question equally good (or bad).

# create a regression model
my_model2 <- lm(points ~ attitude, data = students2014)

# draw diagnostic plots using the plot() function. Choose the plots 1, 2 and 5
plot(my_model2, which=c(1,2,5), par(mfrow = c(2,2)))

Here, in Q-Q plot we see that the points are quite close to the line meaning that the erros is normally distributed (as we are assuming in linear regression). In Residuals vs Fitted values scatter plot we see that the points are allover the plot, not forming a pattern, which means that the error is not depended on explanatory variable (which is good!). Residuals vs Leverage plot we see that there are no observations standing out. This means that there are no single observations pulling the regression line somewhere (causing error). It is a good thing also.

IODS week3 RStudio exercise

Sina Hulkkonen 17/11/2018

Describe the work you have done this week and summarize your learning.

I did all the DataCamp exercises for this week. I think even though I’m having some frustrating moments (I think we all are..?), once I realize I really learned something new, I’m really delighted I took this course. Below are the exercises for this week.

2. Reading the file

library(dplyr)

## Warning: package 'dplyr' was built under R version 3.4.4

## 
## Attaching package: 'dplyr'

## The following object is masked from 'package:GGally':
## 
##     nasa

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

alc<-read.table("http://s3.amazonaws.com/assets.datacamp.com/production/course_2218/datasets/alc.txt", sep=",", header = TRUE)
str(alc)

## 'data.frame':    382 obs. of  35 variables:
##  $ school    : Factor w/ 2 levels "GP","MS": 1 1 1 1 1 1 1 1 1 1 ...
##  $ sex       : Factor w/ 2 levels "F","M": 1 1 1 1 1 2 2 1 2 2 ...
##  $ age       : int  18 17 15 15 16 16 16 17 15 15 ...
##  $ address   : Factor w/ 2 levels "R","U": 2 2 2 2 2 2 2 2 2 2 ...
##  $ famsize   : Factor w/ 2 levels "GT3","LE3": 1 1 2 1 1 2 2 1 2 1 ...
##  $ Pstatus   : Factor w/ 2 levels "A","T": 1 2 2 2 2 2 2 1 1 2 ...
##  $ Medu      : int  4 1 1 4 3 4 2 4 3 3 ...
##  $ Fedu      : int  4 1 1 2 3 3 2 4 2 4 ...
##  $ Mjob      : Factor w/ 5 levels "at_home","health",..: 1 1 1 2 3 4 3 3 4 3 ...
##  $ Fjob      : Factor w/ 5 levels "at_home","health",..: 5 3 3 4 3 3 3 5 3 3 ...
##  $ reason    : Factor w/ 4 levels "course","home",..: 1 1 3 2 2 4 2 2 2 2 ...
##  $ nursery   : Factor w/ 2 levels "no","yes": 2 1 2 2 2 2 2 2 2 2 ...
##  $ internet  : Factor w/ 2 levels "no","yes": 1 2 2 2 1 2 2 1 2 2 ...
##  $ guardian  : Factor w/ 3 levels "father","mother",..: 2 1 2 2 1 2 2 2 2 2 ...
##  $ traveltime: int  2 1 1 1 1 1 1 2 1 1 ...
##  $ studytime : int  2 2 2 3 2 2 2 2 2 2 ...
##  $ failures  : int  0 0 3 0 0 0 0 0 0 0 ...
##  $ schoolsup : Factor w/ 2 levels "no","yes": 2 1 2 1 1 1 1 2 1 1 ...
##  $ famsup    : Factor w/ 2 levels "no","yes": 1 2 1 2 2 2 1 2 2 2 ...
##  $ paid      : Factor w/ 2 levels "no","yes": 1 1 2 2 2 2 1 1 2 2 ...
##  $ activities: Factor w/ 2 levels "no","yes": 1 1 1 2 1 2 1 1 1 2 ...
##  $ higher    : Factor w/ 2 levels "no","yes": 2 2 2 2 2 2 2 2 2 2 ...
##  $ romantic  : Factor w/ 2 levels "no","yes": 1 1 1 2 1 1 1 1 1 1 ...
##  $ famrel    : int  4 5 4 3 4 5 4 4 4 5 ...
##  $ freetime  : int  3 3 3 2 3 4 4 1 2 5 ...
##  $ goout     : int  4 3 2 2 2 2 4 4 2 1 ...
##  $ Dalc      : int  1 1 2 1 1 1 1 1 1 1 ...
##  $ Walc      : int  1 1 3 1 2 2 1 1 1 1 ...
##  $ health    : int  3 3 3 5 5 5 3 1 1 5 ...
##  $ absences  : int  6 4 10 2 4 10 0 6 0 0 ...
##  $ G1        : int  5 5 7 15 6 15 12 6 16 14 ...
##  $ G2        : int  6 5 8 14 10 15 12 5 18 15 ...
##  $ G3        : int  6 6 10 15 10 15 11 6 19 15 ...
##  $ alc_use   : num  1 1 2.5 1 1.5 1.5 1 1 1 1 ...
##  $ high_use  : logi  FALSE FALSE TRUE FALSE FALSE FALSE ...

dim(alc)

## [1] 382  35

This data approach student achievement in secondary education of two Portuguese schools. The data attributes include student grades, demographic, social and school related features) and it was collected by using school reports and questionnaires. Two datasets are provided regarding the performance in two distinct subjects: Mathematics (mat) and Portuguese language (por).There are 382 observations (students) in 35 variables.

3. Hypotheses

I picked up the variables age, sex, studytime and absences. I pickec those up, since we usually adjust with at leat age and sex in epidemiology, and I think alcohol consumption might affect study time and school abscences. My hypotheses are: 1. The older the student, the more he/she consumes alcohol. 2. Boys consume more alcohol than girls. 3. Those cosuming more alcohol study less. 4. Those consuming more alcohol have more school absences.

4. Exploring the hypotheses

library(ggplot2)
library(tableone)

table1<-CreateTableOne(vars = c("age", "sex", "studytime", "absences"), factorVars = c("sex"),strata = c("high_use"), data = alc)
table1

##                        Stratified by high_use
##                         FALSE         TRUE          p      test
##   n                       270           112                    
##   age (mean (sd))       16.51 (1.15)  16.78 (1.21)   0.041     
##   sex = M (%)             113 (41.9)     71 (63.4)  <0.001     
##   studytime (mean (sd))  2.15 (0.86)   1.76 (0.74)  <0.001     
##   absences (mean (sd))   4.23 (6.50)   7.96 (9.33)  <0.001

g3 <- ggplot(alc, aes(x = high_use, y = age, col=sex))
g3 + geom_boxplot() + ylab("age")+ggtitle("Age by alcohol consumption and sex")

g2 <- ggplot(alc, aes(x = high_use, y = studytime, col=sex))
g2 + geom_boxplot() + ylab("studytime")+ggtitle("Study time by alcohol consumption and sex")

g1 <- ggplot(alc, aes(x = high_use, y = absences, col=sex))
g1 + geom_boxplot() + ylab("absences")+ggtitle("Student absences by alcohol consumption and sex")

Looking at these results, it seems that those who consume more alcohol… 1. are the same age as those who don’t BUT girls tend to consume more alcohol younger and boys older. 2. study less (but only in girls) 3. have more school absences, in both sexes.

5. Fitting the logistic regression model

m <- glm(high_use ~ age + sex + +studytime + absences, data = alc, family = "binomial")
summary(m)

## 
## Call:
## glm(formula = high_use ~ age + sex + +studytime + absences, family = "binomial", 
##     data = alc)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -2.6465  -0.8345  -0.5958   1.0875   2.1093  
## 
## Coefficients:
##             Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -3.38942    1.75909  -1.927 0.054004 .  
## age          0.15415    0.10371   1.486 0.137182    
## sexM         0.80051    0.25462   3.144 0.001667 ** 
## studytime   -0.43984    0.16161  -2.722 0.006496 ** 
## absences     0.06621    0.01798   3.683 0.000231 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 462.21  on 381  degrees of freedom
## Residual deviance: 415.46  on 377  degrees of freedom
## AIC: 425.46
## 
## Number of Fisher Scoring iterations: 4

coef(m)

## (Intercept)         age        sexM   studytime    absences 
##  -3.3894221   0.1541471   0.8005131  -0.4398373   0.0662127

OR <- coef(m) %>% exp
CI<-exp(confint(m))

## Waiting for profiling to be done...

cbind(OR, CI)

##                     OR       2.5 %    97.5 %
## (Intercept) 0.03372816 0.001026569 1.0312270
## age         1.16666248 0.953260213 1.4329365
## sexM        2.22668310 1.357240472 3.6904599
## studytime   0.64414120 0.464578524 0.8768517
## absences    1.06845395 1.033661557 1.1089056

In the linear regression model, the odds ratios with 95% confidence for the variables I included in my study hypothesis are: 1. age: OR=1.17 (95% CI=0.00-1.03) 2. sex: OR= 2.23 (95% CI=1.36-3.69) 3. study time: OR=0.64 (95% CI=0.46-0.88) 4. school absences: OR=1.07 (95% CI=1.03-1.11) Interpretation: In this model, age does not predisct high alcohol usage. Male sex does predict, since its 95% CI doesn’t include 1. This means, that males are approximately double the like to high alcohol consumption. Study time had OR under 1 with 95% CI excluding 1; this means that those who study more are less likely to consume more alcohol. The OR for absences was a liitle over 1 with 95% CI excluding 1, meaning that thse who have more study absences are more likely to drink alcohol. If the variable absences was divided differently (not with a range 0-93), but for example in two categories, the OR might be different (I assume larger).

6. Calculating power and error

m <- glm(high_use ~ sex + +studytime + absences, data = alc, family = "binomial")

probabilities <- predict(m, type = "response")

# add the predicted probabilities to 'alc'
alc <- mutate(alc, probability = probabilities)

alc <- mutate(alc, prediction = probability>0.5)

## Warning: package 'bindrcpp' was built under R version 3.4.4

table(high_use = alc$high_use, prediction = alc$prediction)

##         prediction
## high_use FALSE TRUE
##    FALSE   261    9
##    TRUE     85   27

# initialize a plot of 'high_use' versus 'probability' in 'alc'
g <- ggplot(alc, aes(x = probability, y = high_use, col=alc$prediction))

# define the geom as points and draw the plot
g+geom_point()

# tabulate the target variable versus the predictions
table(high_use = alc$high_use, prediction = alc$probability>0.5)%>%prop.table()%>%addmargins()

##         prediction
## high_use      FALSE       TRUE        Sum
##    FALSE 0.68324607 0.02356021 0.70680628
##    TRUE  0.22251309 0.07068063 0.29319372
##    Sum   0.90575916 0.09424084 1.00000000

#defining the function
loss_func <- function(class, prob) {
  n_wrong <- abs(class - prob) > 0.5
  mean(n_wrong)
}

# call loss_func to compute the average number of wrong predictions in the (training) data
loss_func(class = alc$high_use, prob = alc$probability)

## [1] 0.2460733

Interpretation: If the model I built predicts that it is more probable that a student does consume high amount of alcohol, it can find 27 out of 85+27=112 students who really consume hight amount of alcohol. This means that if I had to decide given by these three variables included in the model, this is the odds that I’d succeed in guessing if they consume a lot of alcohol.

The total proportion of inaccurately classified individuals (= the training error) is 24.6%. Manually this is calculated (9+85)/(261+85+9+27) resulting the same as it should be. I think the model did surprisingly well!

7. Bonus: 10-fold cross-validation of the model

# define a loss function (average prediction error)
loss_func <- function(class, prob) {
  n_wrong <- abs(class - prob) > 0.5
  mean(n_wrong)
}

# K-fold cross-validation
library(boot)
cv <- cv.glm(data = alc, cost = loss_func, glmfit = m, K = 10)

# average number of wrong predictions in the cross validation
cv$delta[1]

## [1] 0.2643979

The prediction error in my model is 26.2% (in the DataCamp exercise the error was 25.3%, actually). My model has bigger error, meaning that it is worse than the one used in DataCamp exercises by this means.

I didn’t complete the axtra bonus exercise.

IODS week4 RStudio exercise

Sina Hulkkonen 20/11/2018

Describe the work you have done this week and summarize your learning.

I did all the DataCamp exercises for this week. This week’s exercises reminded me of factor analysis which I’ve done for one article, and I’m getting exited as I realized I might have learnt something new!

2. Data Boston

# access the MASS package
library(MASS)

## 
## Attaching package: 'MASS'

## The following object is masked from 'package:dplyr':
## 
##     select

# load the data
data("Boston")

# explore the dataset
str(Boston)

## 'data.frame':    506 obs. of  14 variables:
##  $ crim   : num  0.00632 0.02731 0.02729 0.03237 0.06905 ...
##  $ zn     : num  18 0 0 0 0 0 12.5 12.5 12.5 12.5 ...
##  $ indus  : num  2.31 7.07 7.07 2.18 2.18 2.18 7.87 7.87 7.87 7.87 ...
##  $ chas   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ nox    : num  0.538 0.469 0.469 0.458 0.458 0.458 0.524 0.524 0.524 0.524 ...
##  $ rm     : num  6.58 6.42 7.18 7 7.15 ...
##  $ age    : num  65.2 78.9 61.1 45.8 54.2 58.7 66.6 96.1 100 85.9 ...
##  $ dis    : num  4.09 4.97 4.97 6.06 6.06 ...
##  $ rad    : int  1 2 2 3 3 3 5 5 5 5 ...
##  $ tax    : num  296 242 242 222 222 222 311 311 311 311 ...
##  $ ptratio: num  15.3 17.8 17.8 18.7 18.7 18.7 15.2 15.2 15.2 15.2 ...
##  $ black  : num  397 397 393 395 397 ...
##  $ lstat  : num  4.98 9.14 4.03 2.94 5.33 ...
##  $ medv   : num  24 21.6 34.7 33.4 36.2 28.7 22.9 27.1 16.5 18.9 ...

summary(Boston)

##       crim                zn             indus            chas        
##  Min.   : 0.00632   Min.   :  0.00   Min.   : 0.46   Min.   :0.00000  
##  1st Qu.: 0.08204   1st Qu.:  0.00   1st Qu.: 5.19   1st Qu.:0.00000  
##  Median : 0.25651   Median :  0.00   Median : 9.69   Median :0.00000  
##  Mean   : 3.61352   Mean   : 11.36   Mean   :11.14   Mean   :0.06917  
##  3rd Qu.: 3.67708   3rd Qu.: 12.50   3rd Qu.:18.10   3rd Qu.:0.00000  
##  Max.   :88.97620   Max.   :100.00   Max.   :27.74   Max.   :1.00000  
##       nox               rm             age              dis        
##  Min.   :0.3850   Min.   :3.561   Min.   :  2.90   Min.   : 1.130  
##  1st Qu.:0.4490   1st Qu.:5.886   1st Qu.: 45.02   1st Qu.: 2.100  
##  Median :0.5380   Median :6.208   Median : 77.50   Median : 3.207  
##  Mean   :0.5547   Mean   :6.285   Mean   : 68.57   Mean   : 3.795  
##  3rd Qu.:0.6240   3rd Qu.:6.623   3rd Qu.: 94.08   3rd Qu.: 5.188  
##  Max.   :0.8710   Max.   :8.780   Max.   :100.00   Max.   :12.127  
##       rad              tax           ptratio          black       
##  Min.   : 1.000   Min.   :187.0   Min.   :12.60   Min.   :  0.32  
##  1st Qu.: 4.000   1st Qu.:279.0   1st Qu.:17.40   1st Qu.:375.38  
##  Median : 5.000   Median :330.0   Median :19.05   Median :391.44  
##  Mean   : 9.549   Mean   :408.2   Mean   :18.46   Mean   :356.67  
##  3rd Qu.:24.000   3rd Qu.:666.0   3rd Qu.:20.20   3rd Qu.:396.23  
##  Max.   :24.000   Max.   :711.0   Max.   :22.00   Max.   :396.90  
##      lstat            medv      
##  Min.   : 1.73   Min.   : 5.00  
##  1st Qu.: 6.95   1st Qu.:17.02  
##  Median :11.36   Median :21.20  
##  Mean   :12.65   Mean   :22.53  
##  3rd Qu.:16.95   3rd Qu.:25.00  
##  Max.   :37.97   Max.   :50.00

Boston is a dataset with 506 observations in 14 variables. It describes the city of Boston, US. There’s information on the city’s economics, pollution and crime rates, for example. The variables are listed below: < code >crim per capita crime rate by town.

< code >zn proportion of residential land zoned for lots over 25,000 sq.ft.

< code >indus proportion of non-retail business acres per town.

< code >chas Charles River dummy variable (= 1 if tract bounds river; 0 otherwise).

< code >nox nitrogen oxides concentration (parts per 10 million).

< code >rm average number of rooms per dwelling.

< code >age proportion of owner-occupied units built prior to 1940.

< code >dis weighted mean of distances to five Boston employment centres.

< code >rad index of accessibility to radial highways.

< code >tax full-value property-tax rate per $10,000.

< code >ptratio pupil-teacher ratio by town.

< code >black 1000(Bk - 0.63)^2 where Bk is the proportion of blacks by town.

< code >lstat lower status of the population (percent).

< code >medv median value of owner-occupied homes in $1000s.

3. Graphical overwiew and correlations

library(tidyr)

## 
## Attaching package: 'tidyr'

## The following object is masked _by_ '.GlobalEnv':
## 
##     table1

library(corrplot)

## corrplot 0.84 loaded

cor_matrix<-cor(Boston) %>% round(digits = 2)

# print the correlation matrix
cor_matrix

##          crim    zn indus  chas   nox    rm   age   dis   rad   tax
## crim     1.00 -0.20  0.41 -0.06  0.42 -0.22  0.35 -0.38  0.63  0.58
## zn      -0.20  1.00 -0.53 -0.04 -0.52  0.31 -0.57  0.66 -0.31 -0.31
## indus    0.41 -0.53  1.00  0.06  0.76 -0.39  0.64 -0.71  0.60  0.72
## chas    -0.06 -0.04  0.06  1.00  0.09  0.09  0.09 -0.10 -0.01 -0.04
## nox      0.42 -0.52  0.76  0.09  1.00 -0.30  0.73 -0.77  0.61  0.67
## rm      -0.22  0.31 -0.39  0.09 -0.30  1.00 -0.24  0.21 -0.21 -0.29
## age      0.35 -0.57  0.64  0.09  0.73 -0.24  1.00 -0.75  0.46  0.51
## dis     -0.38  0.66 -0.71 -0.10 -0.77  0.21 -0.75  1.00 -0.49 -0.53
## rad      0.63 -0.31  0.60 -0.01  0.61 -0.21  0.46 -0.49  1.00  0.91
## tax      0.58 -0.31  0.72 -0.04  0.67 -0.29  0.51 -0.53  0.91  1.00
## ptratio  0.29 -0.39  0.38 -0.12  0.19 -0.36  0.26 -0.23  0.46  0.46
## black   -0.39  0.18 -0.36  0.05 -0.38  0.13 -0.27  0.29 -0.44 -0.44
## lstat    0.46 -0.41  0.60 -0.05  0.59 -0.61  0.60 -0.50  0.49  0.54
## medv    -0.39  0.36 -0.48  0.18 -0.43  0.70 -0.38  0.25 -0.38 -0.47
##         ptratio black lstat  medv
## crim       0.29 -0.39  0.46 -0.39
## zn        -0.39  0.18 -0.41  0.36
## indus      0.38 -0.36  0.60 -0.48
## chas      -0.12  0.05 -0.05  0.18
## nox        0.19 -0.38  0.59 -0.43
## rm        -0.36  0.13 -0.61  0.70
## age        0.26 -0.27  0.60 -0.38
## dis       -0.23  0.29 -0.50  0.25
## rad        0.46 -0.44  0.49 -0.38
## tax        0.46 -0.44  0.54 -0.47
## ptratio    1.00 -0.18  0.37 -0.51
## black     -0.18  1.00 -0.37  0.33
## lstat      0.37 -0.37  1.00 -0.74
## medv      -0.51  0.33 -0.74  1.00

# visualize the correlation matrix
corrplot(cor_matrix, method="circle", type="upper", cl.pos="b", tl.pos="d", tl.cex = 0.6)

The dots represents correlations. The more intense color and the bigger in the dot, the stronger the correlation. Blue means positive and red negative correlation. For example, there is a strong correlation between rad and tax, meaning index of accessibility to radial highways is bigger (easier?) when full-value property-tax rate per $10,000 is greater.

4. Scaling and dividing the data

# center and standardize variables
boston_scaled <- scale(Boston)

# summaries of the scaled variables
summary(boston_scaled)

##       crim                 zn               indus        
##  Min.   :-0.419367   Min.   :-0.48724   Min.   :-1.5563  
##  1st Qu.:-0.410563   1st Qu.:-0.48724   1st Qu.:-0.8668  
##  Median :-0.390280   Median :-0.48724   Median :-0.2109  
##  Mean   : 0.000000   Mean   : 0.00000   Mean   : 0.0000  
##  3rd Qu.: 0.007389   3rd Qu.: 0.04872   3rd Qu.: 1.0150  
##  Max.   : 9.924110   Max.   : 3.80047   Max.   : 2.4202  
##       chas              nox                rm               age         
##  Min.   :-0.2723   Min.   :-1.4644   Min.   :-3.8764   Min.   :-2.3331  
##  1st Qu.:-0.2723   1st Qu.:-0.9121   1st Qu.:-0.5681   1st Qu.:-0.8366  
##  Median :-0.2723   Median :-0.1441   Median :-0.1084   Median : 0.3171  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.:-0.2723   3rd Qu.: 0.5981   3rd Qu.: 0.4823   3rd Qu.: 0.9059  
##  Max.   : 3.6648   Max.   : 2.7296   Max.   : 3.5515   Max.   : 1.1164  
##       dis               rad               tax             ptratio       
##  Min.   :-1.2658   Min.   :-0.9819   Min.   :-1.3127   Min.   :-2.7047  
##  1st Qu.:-0.8049   1st Qu.:-0.6373   1st Qu.:-0.7668   1st Qu.:-0.4876  
##  Median :-0.2790   Median :-0.5225   Median :-0.4642   Median : 0.2746  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.: 0.6617   3rd Qu.: 1.6596   3rd Qu.: 1.5294   3rd Qu.: 0.8058  
##  Max.   : 3.9566   Max.   : 1.6596   Max.   : 1.7964   Max.   : 1.6372  
##      black             lstat              medv        
##  Min.   :-3.9033   Min.   :-1.5296   Min.   :-1.9063  
##  1st Qu.: 0.2049   1st Qu.:-0.7986   1st Qu.:-0.5989  
##  Median : 0.3808   Median :-0.1811   Median :-0.1449  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.: 0.4332   3rd Qu.: 0.6024   3rd Qu.: 0.2683  
##  Max.   : 0.4406   Max.   : 3.5453   Max.   : 2.9865

# class of the boston_scaled object
class(boston_scaled)

## [1] "matrix"

# change the object to data frame
boston_scaled<-as.data.frame(boston_scaled)

# create a quantile vector of crim and print it
bins <- quantile(boston_scaled$crim)

# create a categorical variable 'crime'
crime <- cut(boston_scaled$crim, breaks = bins, include.lowest = TRUE, labels=c("low", "med_low", "med_high", "high"))

# look at the table of the new factor crime
table(crime)

## crime
##      low  med_low med_high     high 
##      127      126      126      127

# remove original crim from the dataset
boston_scaled <- dplyr::select(boston_scaled, -crim)

# add the new categorical value to scaled data
boston_scaled <- data.frame(boston_scaled, crime)

# number of rows in the Boston dataset 
n <- nrow(boston_scaled)

# choose randomly 80% of the rows
ind <- sample(n,  size = n * 0.8)

# create train set
train <- boston_scaled[ind,]

# create test set 
test <- boston_scaled[-ind,]

5. Fittind LDA model on the train data

# linear discriminant analysis
lda.fit <- lda(crime ~ ., data = train)

# print the lda.fit object
lda.fit

## Call:
## lda(crime ~ ., data = train)
## 
## Prior probabilities of groups:
##       low   med_low  med_high      high 
## 0.2425743 0.2500000 0.2351485 0.2722772 
## 
## Group means:
##                   zn      indus          chas        nox         rm
## low       1.06749353 -0.9274591 -0.1116310989 -0.9368884  0.4865313
## med_low  -0.09179412 -0.2811746  0.0005392655 -0.5726678 -0.1288686
## med_high -0.35906012  0.1123097  0.3078751776  0.3908813  0.1379015
## high     -0.48724019  1.0169558 -0.0217863254  1.0903774 -0.4101908
##                 age        dis        rad        tax     ptratio
## low      -0.9205941  0.9282506 -0.6865511 -0.7292187 -0.50263928
## med_low  -0.3473629  0.3521800 -0.5600086 -0.5074507 -0.09653774
## med_high  0.4117150 -0.3799446 -0.4173090 -0.3551634 -0.42677963
## high      0.8310560 -0.8688971  1.6397657  1.5152267  0.78268316
##                black        lstat        medv
## low       0.36807119 -0.789684514  0.58257577
## med_low   0.36224401 -0.135292568  0.03464991
## med_high  0.06608857  0.006646501  0.20507988
## high     -0.81763770  0.906171675 -0.70764241
## 
## Coefficients of linear discriminants:
##                 LD1         LD2          LD3
## zn       0.12009411  0.67454255 -0.894138077
## indus    0.03168523 -0.09600907  0.433158178
## chas    -0.10234269 -0.08156350  0.026791650
## nox      0.36084178 -0.76172873 -1.248251997
## rm      -0.11772261 -0.08677954 -0.206548924
## age      0.22843986 -0.33289466 -0.181137401
## dis     -0.12825937 -0.13708519  0.201152415
## rad      3.43622894  0.89378922 -0.006368736
## tax     -0.01714736  0.06759562  0.446716781
## ptratio  0.12555844  0.05626452 -0.194893397
## black   -0.11641442  0.05014587  0.230204338
## lstat    0.23476983 -0.17325353  0.303554848
## medv     0.20294948 -0.26025337 -0.151985637
## 
## Proportion of trace:
##    LD1    LD2    LD3 
## 0.9556 0.0333 0.0111

# the function for lda biplot arrows
lda.arrows <- function(x, myscale = 1, arrow_heads = 0.1, color = "red", tex = 0.75, choices = c(1,2)){
  heads <- coef(x)
  arrows(x0 = 0, y0 = 0, 
         x1 = myscale * heads[,choices[1]], 
         y1 = myscale * heads[,choices[2]], col=color, length = arrow_heads)
  text(myscale * heads[,choices], labels = row.names(heads), 
       cex = tex, col=color, pos=3)
}

# target classes as numeric
classes <- as.numeric(train$crime)

# plot the lda results
plot(lda.fit, dimen = 2, col=classes,pch=classes)
lda.arrows(lda.fit, myscale = 10)

It looks here, that LD1 explains 94.8% of the variance of the crime classes.

6. Deleting the true values of “crim” and predicting them with LDA model to test data

# save the correct classes from test data
correct_classes <- test$crime

# remove the crime variable from test data
test <- dplyr::select(test, -crime)

# predict classes with test data
lda.pred <- predict(lda.fit, newdata = test)

# cross tabulate the results
table(correct = correct_classes, predicted = lda.pred$class)

##           predicted
## correct    low med_low med_high high
##   low       14      13        2    0
##   med_low    5      15        5    0
##   med_high   0       7       22    2
##   high       0       0        0   17

It looks that the LDA model didn’t predict everything correctly, but was better with “high”" crime rate quintile than the other quintiles. The model predicted 26 cases of “high” (25 correct). But with quintile “low” it had more error, as it predicted 20 out of (20+11=) 31 correct cases. Also, it classified 13 out of (1+13+4=) 18 “med low” and 15 out of (12+15+1=) 28 cases of “med high” correctly.

7. K-means

# access the MASS package
library(MASS)

# load the data
data("Boston")

# explore the dataset
str(Boston)

## 'data.frame':    506 obs. of  14 variables:
##  $ crim   : num  0.00632 0.02731 0.02729 0.03237 0.06905 ...
##  $ zn     : num  18 0 0 0 0 0 12.5 12.5 12.5 12.5 ...
##  $ indus  : num  2.31 7.07 7.07 2.18 2.18 2.18 7.87 7.87 7.87 7.87 ...
##  $ chas   : int  0 0 0 0 0 0 0 0 0 0 ...
##  $ nox    : num  0.538 0.469 0.469 0.458 0.458 0.458 0.524 0.524 0.524 0.524 ...
##  $ rm     : num  6.58 6.42 7.18 7 7.15 ...
##  $ age    : num  65.2 78.9 61.1 45.8 54.2 58.7 66.6 96.1 100 85.9 ...
##  $ dis    : num  4.09 4.97 4.97 6.06 6.06 ...
##  $ rad    : int  1 2 2 3 3 3 5 5 5 5 ...
##  $ tax    : num  296 242 242 222 222 222 311 311 311 311 ...
##  $ ptratio: num  15.3 17.8 17.8 18.7 18.7 18.7 15.2 15.2 15.2 15.2 ...
##  $ black  : num  397 397 393 395 397 ...
##  $ lstat  : num  4.98 9.14 4.03 2.94 5.33 ...
##  $ medv   : num  24 21.6 34.7 33.4 36.2 28.7 22.9 27.1 16.5 18.9 ...

summary(Boston)

##       crim                zn             indus            chas        
##  Min.   : 0.00632   Min.   :  0.00   Min.   : 0.46   Min.   :0.00000  
##  1st Qu.: 0.08204   1st Qu.:  0.00   1st Qu.: 5.19   1st Qu.:0.00000  
##  Median : 0.25651   Median :  0.00   Median : 9.69   Median :0.00000  
##  Mean   : 3.61352   Mean   : 11.36   Mean   :11.14   Mean   :0.06917  
##  3rd Qu.: 3.67708   3rd Qu.: 12.50   3rd Qu.:18.10   3rd Qu.:0.00000  
##  Max.   :88.97620   Max.   :100.00   Max.   :27.74   Max.   :1.00000  
##       nox               rm             age              dis        
##  Min.   :0.3850   Min.   :3.561   Min.   :  2.90   Min.   : 1.130  
##  1st Qu.:0.4490   1st Qu.:5.886   1st Qu.: 45.02   1st Qu.: 2.100  
##  Median :0.5380   Median :6.208   Median : 77.50   Median : 3.207  
##  Mean   :0.5547   Mean   :6.285   Mean   : 68.57   Mean   : 3.795  
##  3rd Qu.:0.6240   3rd Qu.:6.623   3rd Qu.: 94.08   3rd Qu.: 5.188  
##  Max.   :0.8710   Max.   :8.780   Max.   :100.00   Max.   :12.127  
##       rad              tax           ptratio          black       
##  Min.   : 1.000   Min.   :187.0   Min.   :12.60   Min.   :  0.32  
##  1st Qu.: 4.000   1st Qu.:279.0   1st Qu.:17.40   1st Qu.:375.38  
##  Median : 5.000   Median :330.0   Median :19.05   Median :391.44  
##  Mean   : 9.549   Mean   :408.2   Mean   :18.46   Mean   :356.67  
##  3rd Qu.:24.000   3rd Qu.:666.0   3rd Qu.:20.20   3rd Qu.:396.23  
##  Max.   :24.000   Max.   :711.0   Max.   :22.00   Max.   :396.90  
##      lstat            medv      
##  Min.   : 1.73   Min.   : 5.00  
##  1st Qu.: 6.95   1st Qu.:17.02  
##  Median :11.36   Median :21.20  
##  Mean   :12.65   Mean   :22.53  
##  3rd Qu.:16.95   3rd Qu.:25.00  
##  Max.   :37.97   Max.   :50.00

#scale
boston_scaled <- scale(Boston)

# summaries of the scaled variables
summary(boston_scaled)

##       crim                 zn               indus        
##  Min.   :-0.419367   Min.   :-0.48724   Min.   :-1.5563  
##  1st Qu.:-0.410563   1st Qu.:-0.48724   1st Qu.:-0.8668  
##  Median :-0.390280   Median :-0.48724   Median :-0.2109  
##  Mean   : 0.000000   Mean   : 0.00000   Mean   : 0.0000  
##  3rd Qu.: 0.007389   3rd Qu.: 0.04872   3rd Qu.: 1.0150  
##  Max.   : 9.924110   Max.   : 3.80047   Max.   : 2.4202  
##       chas              nox                rm               age         
##  Min.   :-0.2723   Min.   :-1.4644   Min.   :-3.8764   Min.   :-2.3331  
##  1st Qu.:-0.2723   1st Qu.:-0.9121   1st Qu.:-0.5681   1st Qu.:-0.8366  
##  Median :-0.2723   Median :-0.1441   Median :-0.1084   Median : 0.3171  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.:-0.2723   3rd Qu.: 0.5981   3rd Qu.: 0.4823   3rd Qu.: 0.9059  
##  Max.   : 3.6648   Max.   : 2.7296   Max.   : 3.5515   Max.   : 1.1164  
##       dis               rad               tax             ptratio       
##  Min.   :-1.2658   Min.   :-0.9819   Min.   :-1.3127   Min.   :-2.7047  
##  1st Qu.:-0.8049   1st Qu.:-0.6373   1st Qu.:-0.7668   1st Qu.:-0.4876  
##  Median :-0.2790   Median :-0.5225   Median :-0.4642   Median : 0.2746  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.: 0.6617   3rd Qu.: 1.6596   3rd Qu.: 1.5294   3rd Qu.: 0.8058  
##  Max.   : 3.9566   Max.   : 1.6596   Max.   : 1.7964   Max.   : 1.6372  
##      black             lstat              medv        
##  Min.   :-3.9033   Min.   :-1.5296   Min.   :-1.9063  
##  1st Qu.: 0.2049   1st Qu.:-0.7986   1st Qu.:-0.5989  
##  Median : 0.3808   Median :-0.1811   Median :-0.1449  
##  Mean   : 0.0000   Mean   : 0.0000   Mean   : 0.0000  
##  3rd Qu.: 0.4332   3rd Qu.: 0.6024   3rd Qu.: 0.2683  
##  Max.   : 0.4406   Max.   : 3.5453   Max.   : 2.9865

# class of the boston_scaled object
class(boston_scaled)

## [1] "matrix"

# change the object to data frame
boston_scaled<-as.data.frame(boston_scaled)

#calculating the distances
dist_eu <- dist(boston_scaled)

# look at the summary of the distances
summary(dist_eu)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.1343  3.4625  4.8241  4.9111  6.1863 14.3970

#searching for the right number of clusters
set.seed(123)

k_max <- 10

# calculate the total within sum of squares
twcss <- sapply(1:k_max, function(k){kmeans(boston_scaled, k)$tot.withinss})

library(ggplot2)

# visualize the results
qplot(x = 1:k_max, y = twcss, geom = 'line')

# k-means clustering
km <-kmeans(boston_scaled, centers = 2)

# plot the Boston dataset with clusters
pairs(boston_scaled, col = km$cluster)

As wee see in gplot, the line drops most radically, when the number of clusters is 2. In pairs plot, the observations are shown in red or black belonging to each clusted as defined by the variables in the plot.

I didn’t do the bonus exercises.

IODS week5 RStudio exercise

Sina Hulkkonen 1/12/2018

Describe the work you have done this week and summarize your learning.

I did all the DataCamp exercises for this week. For the first time I didn’t make it to the lecture, so I tried to manage myself with the exercises alone.

1. Describing the data

library(GGally)
library(dplyr)
library(corrplot)
library(tidyr)
human<-read.table("http://s3.amazonaws.com/assets.datacamp.com/production/course_2218/datasets/human2.txt", sep=",", header = TRUE)

#summary(human)

ggpairs(human)

# compute the correlation matrix and visualize it with corrplot
cor(human)%>%corrplot()

The ‘human’ dataset originates from the United Nations Development Programme. It contains information on education, birth and maternal mortality rates, life expectancy etc in different countries. In ggpairs plot, we see the distribution in each variable and how the variables correlate with each other. In correlation plot the size of the plot tells about how strong the correlation is, red dots representing negative and blue dots positive correlation. For example, maternal mortality and life expectancy have a strong negative correlation.

2. Principal component analysis (PCA) on the not standardized human data

# perform principal component analysis (with the SVD method)
pca_human <- prcomp(human)

#showing the variance captured by the components
summary(pca_human)

## Importance of components:
##                              PC1      PC2   PC3   PC4   PC5   PC6    PC7
## Standard deviation     1.854e+04 185.5219 25.19 11.45 3.766 1.566 0.1912
## Proportion of Variance 9.999e-01   0.0001  0.00  0.00 0.000 0.000 0.0000
## Cumulative Proportion  9.999e-01   1.0000  1.00  1.00 1.000 1.000 1.0000
##                           PC8
## Standard deviation     0.1591
## Proportion of Variance 0.0000
## Cumulative Proportion  1.0000

# draw a biplot of the principal component representation and the original variables
biplot(pca_human, choices = 1:2, cex = c(0.8, 1), col = c("grey40", "deeppink2"))

## Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], length
## = arrow.len): zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], length
## = arrow.len): zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], length
## = arrow.len): zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], length
## = arrow.len): zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], length
## = arrow.len): zero-length arrow is of indeterminate angle and so skipped

It looks like the component PC1 captures all the variance. This might be due the dataset is not standardized, and the variable variances may vary tremendously, which leads the PCA to think that the variable with the most variance is the most important (although it might not be). This is why the plot is ugly, I think.

3. Principal component analysis (PCA) on the standardized human data

human_std <- scale(human)

# perform principal component analysis (with the SVD method)
pca_human_std <- prcomp(human_std)

#showing the variance captured by the components
summary(pca_human_std)

## Importance of components:
##                           PC1    PC2     PC3     PC4     PC5     PC6
## Standard deviation     2.0708 1.1397 0.87505 0.77886 0.66196 0.53631
## Proportion of Variance 0.5361 0.1624 0.09571 0.07583 0.05477 0.03595
## Cumulative Proportion  0.5361 0.6984 0.79413 0.86996 0.92473 0.96069
##                            PC7     PC8
## Standard deviation     0.45900 0.32224
## Proportion of Variance 0.02634 0.01298
## Cumulative Proportion  0.98702 1.00000

# draw a biplot of the principal component representation and the original variables
biplot(pca_human_std, choices = 1:2, cex = c(0.8, 1), col = c("grey40", "deeppink2"))

Please see the interpretation of the unstandardized data PCA in the previous paraghaph. Now the variance of principal components divides more beatofully, with PC1 capturing 53.6% of the variance and the others less. The plot is prettier. It shows that the arrows form three groups: maternal mortality and adolescent birth rate, percentage of women represantatives in parliament and women:men labour ratio, and the rest of the variables (life expectancy, education rate and ratio and Gross National Income per capita). This tells that they actually might be related and measure a similar feature of the population or country.

4. Interpretation of the previous plot

It is logical that where there are more women involved in working life, they are also more women as parliament representatives. Also, we do know that women give birth younger in developing countries with poorer healthcare systems. In countries where adolescents give birth, there seems to be higher maternal mortality.

5. Tea time!

#install.packages("FactoMineR")
library(FactoMineR)

## Warning: package 'FactoMineR' was built under R version 3.4.4

library(ggplot2)

#getting tea dataset
data("tea")

# look at the summaries and structure of the data
summary(tea)

##          breakfast           tea.time          evening          lunch    
##  breakfast    :144   Not.tea time:131   evening    :103   lunch    : 44  
##  Not.breakfast:156   tea time    :169   Not.evening:197   Not.lunch:256  
##                                                                          
##                                                                          
##                                                                          
##                                                                          
##                                                                          
##         dinner           always          home           work    
##  dinner    : 21   always    :103   home    :291   Not.work:213  
##  Not.dinner:279   Not.always:197   Not.home:  9   work    : 87  
##                                                                 
##                                                                 
##                                                                 
##                                                                 
##                                                                 
##         tearoom           friends          resto          pub     
##  Not.tearoom:242   friends    :196   Not.resto:221   Not.pub:237  
##  tearoom    : 58   Not.friends:104   resto    : 79   pub    : 63  
##                                                                   
##                                                                   
##                                                                   
##                                                                   
##                                                                   
##         Tea         How           sugar                     how     
##  black    : 74   alone:195   No.sugar:155   tea bag           :170  
##  Earl Grey:193   lemon: 33   sugar   :145   tea bag+unpackaged: 94  
##  green    : 33   milk : 63                  unpackaged        : 36  
##                  other:  9                                          
##                                                                     
##                                                                     
##                                                                     
##                   where                 price          age        sex    
##  chain store         :192   p_branded      : 95   Min.   :15.00   F:178  
##  chain store+tea shop: 78   p_cheap        :  7   1st Qu.:23.00   M:122  
##  tea shop            : 30   p_private label: 21   Median :32.00          
##                             p_unknown      : 12   Mean   :37.05          
##                             p_upscale      : 53   3rd Qu.:48.00          
##                             p_variable     :112   Max.   :90.00          
##                                                                          
##            SPC               Sport       age_Q          frequency  
##  employee    :59   Not.sportsman:121   15-24:92   1/day      : 95  
##  middle      :40   sportsman    :179   25-34:69   1 to 2/week: 44  
##  non-worker  :64                       35-44:40   +2/day     :127  
##  other worker:20                       45-59:61   3 to 6/week: 34  
##  senior      :35                       +60  :38                    
##  student     :70                                                   
##  workman     :12                                                   
##              escape.exoticism           spirituality        healthy   
##  escape-exoticism    :142     Not.spirituality:206   healthy    :210  
##  Not.escape-exoticism:158     spirituality    : 94   Not.healthy: 90  
##                                                                       
##                                                                       
##                                                                       
##                                                                       
##                                                                       
##          diuretic             friendliness            iron.absorption
##  diuretic    :174   friendliness    :242   iron absorption    : 31   
##  Not.diuretic:126   Not.friendliness: 58   Not.iron absorption:269   
##                                                                      
##                                                                      
##                                                                      
##                                                                      
##                                                                      
##          feminine             sophisticated        slimming  
##  feminine    :129   Not.sophisticated: 85   No.slimming:255  
##  Not.feminine:171   sophisticated    :215   slimming   : 45  
##                                                              
##                                                              
##                                                              
##                                                              
##                                                              
##         exciting          relaxing              effect.on.health
##  exciting   :116   No.relaxing:113   effect on health   : 66    
##  No.exciting:184   relaxing   :187   No.effect on health:234    
##                                                                 
##                                                                 
##                                                                 
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str(tea)

## 'data.frame':    300 obs. of  36 variables:
##  $ breakfast       : Factor w/ 2 levels "breakfast","Not.breakfast": 1 1 2 2 1 2 1 2 1 1 ...
##  $ tea.time        : Factor w/ 2 levels "Not.tea time",..: 1 1 2 1 1 1 2 2 2 1 ...
##  $ evening         : Factor w/ 2 levels "evening","Not.evening": 2 2 1 2 1 2 2 1 2 1 ...
##  $ lunch           : Factor w/ 2 levels "lunch","Not.lunch": 2 2 2 2 2 2 2 2 2 2 ...
##  $ dinner          : Factor w/ 2 levels "dinner","Not.dinner": 2 2 1 1 2 1 2 2 2 2 ...
##  $ always          : Factor w/ 2 levels "always","Not.always": 2 2 2 2 1 2 2 2 2 2 ...
##  $ home            : Factor w/ 2 levels "home","Not.home": 1 1 1 1 1 1 1 1 1 1 ...
##  $ work            : Factor w/ 2 levels "Not.work","work": 1 1 2 1 1 1 1 1 1 1 ...
##  $ tearoom         : Factor w/ 2 levels "Not.tearoom",..: 1 1 1 1 1 1 1 1 1 2 ...
##  $ friends         : Factor w/ 2 levels "friends","Not.friends": 2 2 1 2 2 2 1 2 2 2 ...
##  $ resto           : Factor w/ 2 levels "Not.resto","resto": 1 1 2 1 1 1 1 1 1 1 ...
##  $ pub             : Factor w/ 2 levels "Not.pub","pub": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Tea             : Factor w/ 3 levels "black","Earl Grey",..: 1 1 2 2 2 2 2 1 2 1 ...
##  $ How             : Factor w/ 4 levels "alone","lemon",..: 1 3 1 1 1 1 1 3 3 1 ...
##  $ sugar           : Factor w/ 2 levels "No.sugar","sugar": 2 1 1 2 1 1 1 1 1 1 ...
##  $ how             : Factor w/ 3 levels "tea bag","tea bag+unpackaged",..: 1 1 1 1 1 1 1 1 2 2 ...
##  $ where           : Factor w/ 3 levels "chain store",..: 1 1 1 1 1 1 1 1 2 2 ...
##  $ price           : Factor w/ 6 levels "p_branded","p_cheap",..: 4 6 6 6 6 3 6 6 5 5 ...
##  $ age             : int  39 45 47 23 48 21 37 36 40 37 ...
##  $ sex             : Factor w/ 2 levels "F","M": 2 1 1 2 2 2 2 1 2 2 ...
##  $ SPC             : Factor w/ 7 levels "employee","middle",..: 2 2 4 6 1 6 5 2 5 5 ...
##  $ Sport           : Factor w/ 2 levels "Not.sportsman",..: 2 2 2 1 2 2 2 2 2 1 ...
##  $ age_Q           : Factor w/ 5 levels "15-24","25-34",..: 3 4 4 1 4 1 3 3 3 3 ...
##  $ frequency       : Factor w/ 4 levels "1/day","1 to 2/week",..: 1 1 3 1 3 1 4 2 3 3 ...
##  $ escape.exoticism: Factor w/ 2 levels "escape-exoticism",..: 2 1 2 1 1 2 2 2 2 2 ...
##  $ spirituality    : Factor w/ 2 levels "Not.spirituality",..: 1 1 1 2 2 1 1 1 1 1 ...
##  $ healthy         : Factor w/ 2 levels "healthy","Not.healthy": 1 1 1 1 2 1 1 1 2 1 ...
##  $ diuretic        : Factor w/ 2 levels "diuretic","Not.diuretic": 2 1 1 2 1 2 2 2 2 1 ...
##  $ friendliness    : Factor w/ 2 levels "friendliness",..: 2 2 1 2 1 2 2 1 2 1 ...
##  $ iron.absorption : Factor w/ 2 levels "iron absorption",..: 2 2 2 2 2 2 2 2 2 2 ...
##  $ feminine        : Factor w/ 2 levels "feminine","Not.feminine": 2 2 2 2 2 2 2 1 2 2 ...
##  $ sophisticated   : Factor w/ 2 levels "Not.sophisticated",..: 1 1 1 2 1 1 1 2 2 1 ...
##  $ slimming        : Factor w/ 2 levels "No.slimming",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ exciting        : Factor w/ 2 levels "exciting","No.exciting": 2 1 2 2 2 2 2 2 2 2 ...
##  $ relaxing        : Factor w/ 2 levels "No.relaxing",..: 1 1 2 2 2 2 2 2 2 2 ...
##  $ effect.on.health: Factor w/ 2 levels "effect on health",..: 2 2 2 2 2 2 2 2 2 2 ...

#too many variables to handle, so I decided to make dataset tea_time
keep_columns <- c("Tea", "How", "how", "sugar", "where", "lunch")

# select the 'keep_columns' to create a new dataset
tea_time <- dplyr::select(tea, one_of(keep_columns))

# look at the summaries and structure of the data
summary(tea_time)

##         Tea         How                      how           sugar    
##  black    : 74   alone:195   tea bag           :170   No.sugar:155  
##  Earl Grey:193   lemon: 33   tea bag+unpackaged: 94   sugar   :145  
##  green    : 33   milk : 63   unpackaged        : 36                 
##                  other:  9                                          
##                   where           lunch    
##  chain store         :192   lunch    : 44  
##  chain store+tea shop: 78   Not.lunch:256  
##  tea shop            : 30                  
##

str(tea_time)

## 'data.frame':    300 obs. of  6 variables:
##  $ Tea  : Factor w/ 3 levels "black","Earl Grey",..: 1 1 2 2 2 2 2 1 2 1 ...
##  $ How  : Factor w/ 4 levels "alone","lemon",..: 1 3 1 1 1 1 1 3 3 1 ...
##  $ how  : Factor w/ 3 levels "tea bag","tea bag+unpackaged",..: 1 1 1 1 1 1 1 1 2 2 ...
##  $ sugar: Factor w/ 2 levels "No.sugar","sugar": 2 1 1 2 1 1 1 1 1 1 ...
##  $ where: Factor w/ 3 levels "chain store",..: 1 1 1 1 1 1 1 1 2 2 ...
##  $ lunch: Factor w/ 2 levels "lunch","Not.lunch": 2 2 2 2 2 2 2 2 2 2 ...

# visualize the dataset
gather(tea_time) %>% ggplot(aes(value)) + facet_wrap("key", scales = "free") + geom_bar()+theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 8))

## Warning: attributes are not identical across measure variables;
## they will be dropped

# multiple correspondence analysis
mca <- MCA(tea_time, graph = FALSE)

# summary of the model
summary(mca)

## 
## Call:
## MCA(X = tea_time, graph = FALSE) 
## 
## 
## Eigenvalues
##                        Dim.1   Dim.2   Dim.3   Dim.4   Dim.5   Dim.6
## Variance               0.279   0.261   0.219   0.189   0.177   0.156
## % of var.             15.238  14.232  11.964  10.333   9.667   8.519
## Cumulative % of var.  15.238  29.471  41.435  51.768  61.434  69.953
##                        Dim.7   Dim.8   Dim.9  Dim.10  Dim.11
## Variance               0.144   0.141   0.117   0.087   0.062
## % of var.              7.841   7.705   6.392   4.724   3.385
## Cumulative % of var.  77.794  85.500  91.891  96.615 100.000
## 
## Individuals (the 10 first)
##                       Dim.1    ctr   cos2    Dim.2    ctr   cos2    Dim.3
## 1                  | -0.298  0.106  0.086 | -0.328  0.137  0.105 | -0.327
## 2                  | -0.237  0.067  0.036 | -0.136  0.024  0.012 | -0.695
## 3                  | -0.369  0.162  0.231 | -0.300  0.115  0.153 | -0.202
## 4                  | -0.530  0.335  0.460 | -0.318  0.129  0.166 |  0.211
## 5                  | -0.369  0.162  0.231 | -0.300  0.115  0.153 | -0.202
## 6                  | -0.369  0.162  0.231 | -0.300  0.115  0.153 | -0.202
## 7                  | -0.369  0.162  0.231 | -0.300  0.115  0.153 | -0.202
## 8                  | -0.237  0.067  0.036 | -0.136  0.024  0.012 | -0.695
## 9                  |  0.143  0.024  0.012 |  0.871  0.969  0.435 | -0.067
## 10                 |  0.476  0.271  0.140 |  0.687  0.604  0.291 | -0.650
##                       ctr   cos2  
## 1                   0.163  0.104 |
## 2                   0.735  0.314 |
## 3                   0.062  0.069 |
## 4                   0.068  0.073 |
## 5                   0.062  0.069 |
## 6                   0.062  0.069 |
## 7                   0.062  0.069 |
## 8                   0.735  0.314 |
## 9                   0.007  0.003 |
## 10                  0.643  0.261 |
## 
## Categories (the 10 first)
##                        Dim.1     ctr    cos2  v.test     Dim.2     ctr
## black              |   0.473   3.288   0.073   4.677 |   0.094   0.139
## Earl Grey          |  -0.264   2.680   0.126  -6.137 |   0.123   0.626
## green              |   0.486   1.547   0.029   2.952 |  -0.933   6.111
## alone              |  -0.018   0.012   0.001  -0.418 |  -0.262   2.841
## lemon              |   0.669   2.938   0.055   4.068 |   0.531   1.979
## milk               |  -0.337   1.420   0.030  -3.002 |   0.272   0.990
## other              |   0.288   0.148   0.003   0.876 |   1.820   6.347
## tea bag            |  -0.608  12.499   0.483 -12.023 |  -0.351   4.459
## tea bag+unpackaged |   0.350   2.289   0.056   4.088 |   1.024  20.968
## unpackaged         |   1.958  27.432   0.523  12.499 |  -1.015   7.898
##                       cos2  v.test     Dim.3     ctr    cos2  v.test  
## black                0.003   0.929 |  -1.081  21.888   0.382 -10.692 |
## Earl Grey            0.027   2.867 |   0.433   9.160   0.338  10.053 |
## green                0.107  -5.669 |  -0.108   0.098   0.001  -0.659 |
## alone                0.127  -6.164 |  -0.113   0.627   0.024  -2.655 |
## lemon                0.035   3.226 |   1.329  14.771   0.218   8.081 |
## milk                 0.020   2.422 |   0.013   0.003   0.000   0.116 |
## other                0.102   5.534 |  -2.524  14.526   0.197  -7.676 |
## tea bag              0.161  -6.941 |  -0.065   0.183   0.006  -1.287 |
## tea bag+unpackaged   0.478  11.956 |   0.019   0.009   0.000   0.226 |
## unpackaged           0.141  -6.482 |   0.257   0.602   0.009   1.640 |
## 
## Categorical variables (eta2)
##                      Dim.1 Dim.2 Dim.3  
## Tea                | 0.126 0.108 0.410 |
## How                | 0.076 0.190 0.394 |
## how                | 0.708 0.522 0.010 |
## sugar              | 0.065 0.001 0.336 |
## where              | 0.702 0.681 0.055 |
## lunch              | 0.000 0.064 0.111 |

# visualize MCA
plot(mca, invisible=c("ind"), habillage="quali")

# visualize MCA
plot(mca, invisible=c("var"), habillage="quali")

I decided to keep only some variables in the dataset, since there were too many in the original dataset. MCA is run for my dataset. I printed out both variables and individuals. The first plot (individuals) is informative and tells us which variable factors represent each other. For example, individuals that buy unpacked tea are likely to buy it from tea shop (see the factors levels nearby each other in the plot).

IODS course project

Sina Hulkkonen

About the project

IODS week2 RStudio exercise

IODS week3 RStudio exercise

2. Reading the file

3. Hypotheses

4. Exploring the hypotheses

5. Fitting the logistic regression model

6. Calculating power and error

7. Bonus: 10-fold cross-validation of the model

IODS week4 RStudio exercise

2. Data Boston

3. Graphical overwiew and correlations

4. Scaling and dividing the data

5. Fittind LDA model on the train data

6. Deleting the true values of “crim” and predicting them with LDA model to test data

7. K-means

IODS week5 RStudio exercise

1. Describing the data

2. Principal component analysis (PCA) on the not standardized human data

3. Principal component analysis (PCA) on the standardized human data

4. Interpretation of the previous plot

5. Tea time!